THIS INVESTIGATOR GARY STORMO, UNIVERSITY OF COLORADO AT BOULDER PROPOSES THE APPLICATION AND SOME FURTHER DEVELOPMENT OF A SERIES OF METHODS BASED ON A SIMILAR SET OF PRINCIPLES WHICH EXTRACT AND UTILIZE MOTIFS COMMON TO A SET OF EXAMPLE SEQUENCES. THESE METHODS EXPLORE ALIGNMENTS BETWEEN EXAMPLES EXHIBITING THE PATTERN AND REFINE THE DEFINITION OF THE MOTIF FROM THE MANY OCCURRENCES. THIS A VERY POWERFUL TECHNIQUE WITH MANY POTENTIAL APPLICATIONS FOR THE DISCOVERY OF NEW PATTERNS, AS WELL AS THE RECOGNITION OF NEW MEMBERS OF KNOWN PATTERN FAMILIES. EXAMPLES INCLUDE, SEQUENCE COMPARISON USING HMMS OR PROFILES CONSTRUCTED FROM PROTEIN FAMILIES, RECOGNITION OF NEW TRANSCRIPTION FACTOR BINDING SITES FROM MULTIPLE EXAMPLES OF CO-REGULATED GENES, RECOGNITION OF MOTIFS IN RNAS RELATED TO DEGRADATION OR STRUCTURAL SIGNALS, AND METHODS FOR IDENTIFYING MOTIFS IN PROTEINS RELATED TO CELLULAR LOCALIZATION.